Members of the large serine recombinase (LSR) family of enzymes carry out recombination between short, specific DNA sequences commonly referred to as attP and attB. For many LSR enzymes, the reaction is effectively irreversible and does not require accessory proteins, additional DNA elements, or other cofactors. These features have led to the emergence of LSRs as important new tools that can carry out precise manipulations of eukaryotic genomes and show promise in gene therapy applications. Despite the importance of the LSRs, our current mechanistic understanding of how these enzymes function is limited. There are no structural models available for any LSR protein and no indication of how the recombinases bind to the attP and attB recombination sites. It has therefore been difficult to understand how the LSR enzymes exhibit such high site selectivity and strong directionality. To address these gaps in our understanding of LSR structure and function, we will use the bacteriophage A118 integrase as a model system to (i) test a mechanism where LSR enzymes use an unusual, extended coiled-coil motif to regulate the recombination reaction, and (ii) develop a structural and energetic framework for understanding selective association, or synapsis, of the recombining sites. Our functional model for LSR regulation of site-specificity and directionality is inspired by a A118 integrase-DNA complex structure that we have recently determined. These studies will provide an important framework for our long-term goal engineering LSRs to integrate preferentially into a single site in the human genome.